track chain_cs10
bigDataUrl bbi/cs10.bigChain.bb
linkDataUrl bbi/cs10.bigLink.bb
shortLabel cs10 chain
longLabel cs10 aligned to JL_Mother
type bigChain
visibility pack
group compGeno
priority 7

track rbest_cs10
bigDataUrl bbi/cs10.rbestChain.bb
linkDataUrl bbi/cs10.rbestLink.bb
shortLabel cs10 rbest
longLabel cs10 reciprocal-best chains to JL_Mother
type bigChain
visibility hide
group compGeno
priority 9

track JL_Mother_cs10genes
bigDataUrl bbi/cs10.genes.bb
shortLabel Genes from cs10
longLabel cs10 RefSeq gene models lifted onto JL_Mother through the cs10 chain (not its own annotation)
type bigBed 12
visibility hide
group genes

track cytoBandIdeo
bigDataUrl bbi/JL_Mother.cytoBand.bb
shortLabel Chromosome Band (Ideogram)
longLabel Ideogram for Orientation
type bigBed 4 +
visibility dense
group map

track JL_Mother_gc
bigDataUrl bbi/JL_Mother.gc.bw
shortLabel GC Percent
longLabel GC percent of JL_Mother over non-N bases
type bigWig 0 100
viewLimits 25:55
autoScale off
windowingFunction mean
graphTypeDefault bar
maxHeightPixels 128:36:16
color 0,0,0
altColor 128,128,128
visibility dense
group map

track repeats
superTrack on show
shortLabel Repeats
longLabel Repeat annotation and masking for JL_Mother
group varRep

track JL_Mother_maskunion
parent repeats
bigDataUrl bbi/JL_Mother.maskunion.bb
shortLabel Aligner mask
longLabel Union of our four maskers: the soft-masking every panel alignment ran on
type bigBed 3
visibility dense
group varRep
priority 2

track JL_Mother_dustmasker
parent repeats
bigDataUrl bbi/JL_Mother.dustmasker.bb
shortLabel dustmasker
longLabel dustmasker (low-complexity), WF-B
type bigBed 3
visibility hide
group varRep

track JL_Mother_windowmasker
parent repeats
bigDataUrl bbi/JL_Mother.windowmasker.bb
shortLabel WindowMasker
longLabel WindowMasker (over-represented k-mers), WF-B
type bigBed 3
visibility hide
group varRep

track JL_Mother_tantan
parent repeats
bigDataUrl bbi/JL_Mother.tantan.bb
shortLabel tantan
longLabel tantan (tandem repeats), WF-B
type bigBed 3
visibility hide
group varRep

track JL_Mother_fastan
parent repeats
bigDataUrl bbi/JL_Mother.fastan.bb
shortLabel FasTAN
longLabel FasTAN (satellite and long tandem arrays), WF-B
type bigBed 3
visibility hide
group varRep

track assembly
longLabel Assembly (UCSC GenArk)
shortLabel Assembly
visibility hide
colorByStrand 150,100,30 230,170,40
color 150,100,30
altColor 230,170,40
bigDataUrl bbi/genark.assembly.bb
type bigBed 6
html bbi/genark.assembly
searchIndex name
searchTrix bbi/genark.assembly.ix
url https://www.ncbi.nlm.nih.gov/nuccore/$$
urlLabel NCBI Nucleotide database:
group map

track tanDups
shortLabel Tandem Dups
longLabel Paired identical sequences (UCSC GenArk)
compositeTrack on
visibility hide
type bigBed 12
group map
html bbi/genark.tanDups

track tandemDups
parent tanDups on
shortLabel Tandem Dups
longLabel Paired exactly identical sequence survey over entire genome assembly
bigDataUrl bbi/genark.tandemDups.bb
type bigBed 12

track repeatMasker
shortLabel RepeatMasker
longLabel RepeatMasker Repetitive Elements (UCSC GenArk)
type bigRmsk 9 +
visibility pack
group varRep
bigDataUrl bbi/genark.rmsk.bb
maxWindowToDraw 5000000
html bbi/genark.repeatMasker

track simpleRepeat
shortLabel Simple Repeats
longLabel Simple Tandem Repeats by TRF (UCSC GenArk)
group varRep
visibility dense
type bigBed 4 +
bigDataUrl bbi/genark.simpleRepeat.bb
html bbi/genark.simpleRepeat

track ncbiGene
longLabel Gene models submitted to GenBank, ENA, DDBJ (UCSC GenArk)
shortLabel NCBI GenBank
visibility pack
color 0,80,150
altColor 150,80,0
colorByStrand 0,80,150 150,80,0
bigDataUrl bbi/genark.ncbiGene.bb
type bigGenePred
urls name2="https://www.ncbi.nlm.nih.gov/gene/?term=$$" geneName="https://www.ncbi.nlm.nih.gov/gene/$$" geneName2="https://www.ncbi.nlm.nih.gov/nuccore/$$"
html bbi/genark.ncbiGene
searchIndex name
searchTrix bbi/genark.ncbiGene.ix
urlLabel Entrez gene:
labelFields geneName,geneName2
defaultLabelFields geneName2
group genes

track augustus
shortLabel Augustus
longLabel Augustus Gene Predictions (UCSC GenArk)
group genes
visibility dense
color 180,0,0
type bigGenePred
bigDataUrl bbi/genark.augustus.bb
html bbi/genark.augustus

track xenoRefGene
shortLabel RefSeq mRNAs
longLabel RefSeq mRNAs mapped to this assembly (UCSC GenArk)
group rna
visibility pack
color 180,0,0
type bigGenePred
bigDataUrl bbi/genark.xenoRefGene.bb
url https://www.ncbi.nlm.nih.gov/nuccore/$$
urlLabel NCBI Nucleotide database:
labelFields name,geneName,geneName2
defaultLabelFields geneName
searchIndex name
searchTrix bbi/genark.xenoRefGene.ix
html bbi/genark.xenoRefGene